runner Robert Bruce, and Bunce went aboard Robert Bruce as prize master and commanded her on her voyage to New York City, where she arrived on 1 November 1862. After detaching from Penobscot, Bunce became executive officer of the sloop-of-war , then refitting at Philadelphia. He remained aboard Pawnee after her refit was completed as she joined the South Atlantic Blockading Squadron off Stono River, South Carolina. Promoted to lieutenant commander on 10 January 1863 while aboard Pawnee, he oversaw the sounding, buoying, and removal of obstructions that winter in interior channels between Stono River and Morris Island in the outer reaches of Charleston Harbor. He then became aide to Brigadier General Quincy A. Gillmore and took charge of the disembarkation of the five regiments of Brigadier General George C. Strong's brigade through the channels he had cleared. Bunce commanded the naval portion of the attack on Morris Island that resulted in its capture except for its northern tip, which was controlled by Confederate Fort Wagner. For his actions at Morris Island he received an honorable mention in the report on the action of Commander George Balch and Rear Admiral John A. Dahlgren to the United States Department of the Navy. Bunce then left Pawnee and reported aboard the monitor . While aboard Patapsco, Bunce took part in her many exchanges of gunfire with Confederate forces during the siege of Charleston in 1863. On the night of 8–9 September 1863, he participated in a night boat attack on Fort Sumter by a force of U.S. Navy and United States Marine Corps personnel under the overall command of Patapscos commanding officer, Commander Thomas H. Stevens, Jr.; although the attack was a fiasco, Stevens gave Bunce an honorable mention in his report on the attack. In November 1863, Bunce suffered injuries when a cartridge detonated prematurely in a gun turret aboard Patapsco while she was in action against Confederate forces. As a result, he was detached from Patapsco and ordered to the steam screw frigate to convalesce. He reported aboard the monitor for temporary duty on 8 December 1863, but returned to Wabash on 7 January 1864. In January 1864, Bunce received another temporary assignment, this time to command the monitor , then returned to Wabash. He then was assigned to the staff of Rear Admiral Dahlgren, the commander of the South Atlantic Blockading Squadron, serving as "Chief of Scouts" and in